AMBER Archive (2004)

Subject: Re: AMBER: Parameters for nonpolar contribution to solvation

From: Holger Gohlke (gohlke_at_bioinformatik.uni-frankfurt.de)
Date: Sat Apr 24 2004 - 07:06:34 CDT

Thomas Steinbrecher schrieb:
>
> Dear Amber users,
>
> I have noticed that the results when running mm_pbsa_statistics.pl
> independently on the *.all.out files from a mm_pbsa calculation, the
> resulting binding free energies differ in the PBSUR part, the hydrophobic
> contribution to the binding free energy.
>
> The cause of that seems to me that if mm_pbsa_statistics.pl is used,
> PBSUR is calculated always with the gamma and beta parammeters set to
> 0.00542 and 0.92, while mm_pbsa.pl uses the gamma and beta parameters as
> set in the input file. The default parameters for gamma and beta in
> mm_pbsa.in have changed to 0.005 and 0.0 in amber8.
>
> My two questions are:
>
> Is this correct and should mm_pbsa_statistics.pl be changed to accept
> different values for gamma and beta?

This is true, there is an inconsistency with respect to the choice of
default parameters for beta and gamma in the mm_pbsa.in file and the
mm_pbsa_statistics.pm . Thank you for pointing this out.

The "old" values 0.00542/0.92 are valid if one wants to calculate the
nonpolar part to solvation free energy in connection with the PARSE
parameter set for the polar part. The "new" values 0.005/0.0 are meant
to be used together with the optimized cavity radii available within the
"pbsa" module of AMBER. (Please note that you also have to adapt the
radius of the probe in this case.)

> Should one use the new parameters for calcuations of ligand binding
> free energies or the old ones, or what is the motivation of the change?

The proper choice of beta/gamma values depends on which parameter set
you use for calculating the polar part to solvation free energy.

Best regards

Holger

>
> Kind Regards,
>
> Thomas
>
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-- 
!!!      Please note new telephone number      !!!
++++++++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke

J.W. Goethe-Universität
Fachbereich Biologie und Informatik
Institut für Mikrobiologie	
Marie-Curie-Str. 9              
60439 Frankfurt/Main            
Germany                         

Tel.:  (+49) 69-798-29411; Fax: (+49) 69-798-29826
Email: gohlke_at_bioinformatik.uni-frankfurt.de
URL:   http://www.rz.uni-frankfurt.de/~hgohlke
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